Evidence map›Paper›PMID 38916266›Full record

ArticleThe Journal of chemical physics2024

Broadening access to small-molecule parameterization with the force field toolkit.

Yunlin Zeng, Anna Pavlova, Philip M Nelson, Zachary L Glick, Lan Yang, Yui Tik Pang, Mariano Spivak, Giuseppe Licari, Emad Tajkhorshid, C David Sherrill and 1 more

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Yunlin ZengSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0003-4594-4331
Anna PavlovaSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-6527-944X
Philip M NelsonCenter for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0001-5102-7797
Zachary L GlickCenter for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0003-0900-2849
Lan YangSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-8664-8929
Yui Tik PangSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0003-4843-4468
Mariano SpivakTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.ORCID 0000-0003-2249-119X
Giuseppe LicariTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.ORCID 0000-0002-8490-7536
Emad TajkhorshidTheoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.ORCID 0000-0001-8434-1010
C David SherrillCenter for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-5570-7666
James C GumbartSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.ORCID 0000-0002-1510-7842

Funding

WHOLE CELL SIMULATIONP41GM104601 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI TAJKHORSHID, EMAD · 2012 to 2021
$19.0M
Resource for Macromolecular Modeling and VisualizationR24GM145965 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Emad Tajkhorshid · 2022 to 2026
$6.2M
Altering Hepatitis B Virus assembly through pharmacological interventionR01AI148740 · NIAID · GEORGIA INSTITUTE OF TECHNOLOGY · PI GUMBART, JAMES C. · 2020 to 2024
$2.0M
NIAID NIH HHS R01 AI148740NIGMS NIH HHS P41 GM104601NIGMS NIH HHS R24 GM145965
6 · The paper itself

Abstract

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.

Identifiers

PMID38916266
PMCPMC11531335

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.